get.conservative.fold.enrichment.profile: Estimate minimal fold enrichment/depletion along the...

In spp: ChIP-Seq Processing Pipeline

Description

The method provides a statistical assessment of enrichment/depletion along the chromosomes. To assess tag density enrichment/depletion, a sliding window of a specified size (fws) is used to calculate the density of the foreground tags (ftl). Multiple, typically larger windows are used to estimate background tag (btl) density around the same location. The densities are compared as ratios of two Poisson processes to estimate lower bound of foreground enrichment, or upper bound of foreground depletion. If multiple window sizes were used to estimate the background tag density, the most conservative one is chosen for each point.

Usage

  get.conservative.fold.enrichment.profile(ftl, 
    btl, 
    fws, 
    bwsl = c(1, 5, 25, 50) * fws, 
    step = 50, 
    tag.shift = 146/2, 
    alpha = 0.05, 
    use.most.informative.scale = F, 
    quick.calculation = T,
    background.density.scaling = T, 
    bg.weight = NULL, 
    posl= NULL, 
    return.mle = F)

Arguments

ftl	foreground tag vector list
btl	background tag vector list
fws	foreground window size
bwsl	background window scales. The size(s) of background windows will be fws*bwsl.
step	spacing between positions at which the enrichment/depletion is evaluated
tag.shift	number of basepairs by which positive and negative tag coordinates should be shifted towards eachother (half of binding peak separation distance)
alpha	desired level of statistical significance
use.most.informative.scale	for each position, instead of evaluating enrichment ratio bounds for all background window scales, choose the one with the highest observed density to speed up the calculations
quick.calculation	Use square root transformation method instead of a Bayesian method. This speeds up the caclulation considerably and is turned on by default.
background.density.scaling	If TRUE, regions of significant tag enrichment will be masked out when calculating size ratio of the signal to control datasets (to estimate ratio of the background tag density). If FALSE, the dataset ratio will be equal to the ratio of the number of tags in each dataset.
bg.weight	optional weight by which the background density should be multipled for scaling. If not supplied, the weight is calculated based on the ratio of the reduced ChIP to input dataset sizes.
posl	posl
return.mle	return.mle

Value

A list of elements corresponding to chromosomes, with each element being an $x/$y data.frame giving the position and the log2 conservative estimate of enrichment/depletion fold ratios around that position. Use writewig to output the structure to a WIG file.

References

R.M.Price, D.G. Bonett "Estimating the ratio fo two Poisson rates", Comp. Stat & Data Anal. 32(2000) 345

See Also

get.smoothed.tag.density

Examples

## Not run: 
    enrichment.estimates <- get.conservative.fold.enrichment.profile(chip.data,
      input.data,
      fws=2*binding.characteristics$whs,
      step=100,
      alpha=0.01);
    writewig(enrichment.estimates,
      "example.enrichment.estimates.wig",
      "Example conservative fold-enrichment/depletion estimates shown on log2 scale");
  
## End(Not run)

spp documentation built on May 30, 2019, 5:03 p.m.